AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_mjan_reg_100.orf -o146_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ08206 98 M_jannaschii_chromosome #2 RMJ10471 175 M_jannaschii_chromosome #3 RMJ03238 201 M_jannaschii_chromosome #4 RMJ13747 52 M_jannaschii_chromosome #5 RMJ00104 143 M_jannaschii_chromosome Motif number 1 ATTATTCAGAAACCATAGGGCTTCGCCCTA 1 24 1 AACCATAGGG 0.980439 -75 TCCTGGGTATCCCAATAGGGCGAAGCCCTA 1 39 0 CCCAATAGGG 0.712254 -60 GCTACATTGTATCCATAGGGGAAACCCCCT 2 19 1 ATCCATAGGG 0.97519 -157 AAAGGTTCATCCCAATAGGGGGTTTCCCCT 2 35 0 CCCAATAGGG 0.712254 -141 TGGGGAGTATCCCAATAGAGGGGCGAAGCC 2 131 1 CCCAATAGAG 0.914626 -45 TCTGTATAAGACCCATAGAGGGGCTTCGCC 2 152 0 ACCCATAGAG 0.991646 -24 TGGATACTTCACTGATAGGGACTATAAACG 3 42 1 ACTGATAGGG 0.962401 -160 TTGAACGAAAACTCTTAGAGTTTTCATAGC 3 88 1 ACTCTTAGAG 0.864375 -114 ********** Masking position 7 Map Score: 15.7093 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 49 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 2 CCAAAACCTAACACCTCCTCGCTTACGCTCGG 2 79 1 ACACCTCCGC 0.999552 -97 TTACTAATTTACACCTCCGAGCGTAAGCGAGG 2 95 0 ACACCTCCGC 0.999547 -81 TCAAAAACTAACACCTCCTCGCTTCGCTCGGA 3 142 1 ACACCTCCGC 0.999552 -60 TTGTAAATTTACACTTCCGAGCGAAGCGAGGA 3 157 0 ACACTTCCGC 0.998218 -45 ******** ** Masking position 6 Map Score: 11.5852 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 0 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AGAAACCATAGGGCTTCGCCCTATTGGGAT 1 31 1 GGGCTTCGCC 0.99613 -68 AATGCATCCTGGGTATCCCAATAGGGCGAA 1 45 0 GGGTATCCCA 0.963678 -54 TCCCAATAGGGGGTTTCCCCTATGGATACA 2 26 0 GGGTTTCCCC 0.979252 -150 CTTTTAGTAAAAGCTTCACCAAAACCTAAC 2 61 1 AAGCTTCACC 0.96119 -115 AAGATTTGGGGAGTATCCCAATAGAGGGGC 2 125 1 GAGTATCCCA 0.953664 -51 ACCCATAGAGGGGCTTCGCCCCTCTATTGG 2 142 0 GGGCTTCGCC 0.99613 -34 AAGCATCACCCAGATTTTAT 3 192 0 AAGCATCACC 0.950041 -10 ********** Masking position 6 Map Score: 11.2989 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 21 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TATGGATACAATGTAGCTTTTCATT 2 5 0 ATGTAGTTTT 0.949647 -171 AGCGAGGAGGTGTTAGGTTTTGGTGAAGCTT 2 71 0 TGTTAGTTTT 0.961634 -105 CCTCACCCAGATTTTTATTTTAATATTT 3 8 0 ATTTTTTTTT 0.856025 -194 AGCGAGGAGGTGTTAGTTTTTGATGAAATGG 3 134 0 TGTTAGTTTT 0.961634 -68 CCATTTTGATTTTTTGTCTAATT 5 3 1 ATTTTGTTTT 0.962956 -141 TTTTTGTCTAATTTAGTTTTACGCTTCAAAT 5 21 1 ATTTAGTTTA 0.92714 -123 TCAAATTAATATTTATGTTTTTAATAGCTTT 5 46 1 ATTTATTTTT 0.941999 -98 TTTTAATAGCTTTTAGCTTTTTGGTTGCTAA 5 64 1 TTTTAGTTTT 0.977907 -80 ****** **** Masking position 4 Map Score: 8.90779 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 349 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 GATACCCAGGATGCATTGCTTCTGCAAAGA 1 58 1 ATGCATTGCT 0.979257 -41 AAATTTTAAGAGGCATTGCTTCTTTGCAGA 1 78 0 AGGCATTGCT 0.972216 -21 AATGAAAAGCTACATTGTATC 2 2 1 ATGAAAAGCT 0.958239 -174 TGAACCTTTTAGTAAAAGCTTCACCAAAAC 2 56 1 AGTAAAAGCT 0.901986 -120 CTCTTAGAGTTTTCATAGCTGGAAAGCATA 3 99 1 TTTCATAGCT 0.958241 -103 CATAGCTGGAAAGCATAGCTCTCCATTTCA 3 112 1 AAGCATAGCT 0.970678 -90 TATTTATGTTTTTAATAGCTTTTAGCTTTT 5 55 1 TTTAATAGCT 0.917425 -89 ********** Masking position 5 Map Score: 5.85193 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 132 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AGCCCTATGGTTTCTGAATAATTCTTTCATCAT 1 13 0 TTTCTGAAAT 0.956263 -86 GGGATGAACCTTTTAGTAAAAGCTTCACCAAAA 2 52 1 TTTTAGTAAC 0.921146 -124 TAAACGAAACTTTTAGAAAAAGTTGAACGAAAA 3 66 1 TTTTAGAAAT 0.983418 -136 GAGGTGTTAGTTTTTGATGAAATGGAGAGCTAT 3 126 0 TTTTTGAAAT 0.983294 -76 CCCTCCAATCTTTTAGAGAAAGTTAAATAGAA 4 10 0 TTTTAGAAAT 0.983418 -43 CCATTTTGATTTTTTGTCTAATTTAGTTTTACG 5 11 1 TTTTTGTAAT 0.961711 -133 ******* ** * Masking position 10 Map Score: 4.56486 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 101 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 AGCAATGCCTCTTAAAATTTA 1 88 1 CTTAAAATTT 0.803828 -11 GAAGCTTTTACTAAAAGGTTCATCCCAATA 2 48 0 CTAAAAGGTT 0.984369 -128 TCAACTTTTTCTAAAAGTTTCGTTTATAGT 3 62 0 CTAAAAGTTT 0.990772 -140 TATGAAAACTCTAAGAGTTTTCGTTCAACT 3 86 0 CTAAGAGTTT 0.975159 -116 TTAACTTTCTCTAAAAGATTGGAGGGAGAA 4 17 1 CTAAAAGATT 0.977007 -36 AACCAAAAAGCTAAAAGCTATTAAAAACAT 5 60 0 CTAAAAGCTA 0.939528 -84 ********** Masking position 6 Map Score: 6.16683 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 82 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 GAAGCAATGCATCCTGGGTATCCCAATAGG 1 50 0 ATCCTGGGTA 0.976499 -49 TTAAAATAAAAATCTGGGTGAGGATATGGA 3 16 1 AATCTGGGTG 0.995411 -186 CAACTGATAAAATCTGGGTGATGCTT 3 186 1 AATCTGGGTG 0.995411 -16 ********** Masking position 1 Map Score: 1.30972 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: -1.36181e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -1.36181e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: -1.36181e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0